david_stoolA_otus: David Stool Sequencing Data for Subject A

In hallucigenia-sparsa/seqtime: Time Series Analysis of Sequencing Data

David Stool Sequencing Data for Subject A

Description

The OTUs sequenced from stool samples of subject A over time.

Usage

data(david_stoolA_otus)

Format

An object of class data.frame with 5431 rows and 329 columns.

Details

Subject A traveled from day 71 to day 122 and contracted diarrhea on days 80 to 85 and 104 to 113.

Value

OTUxSample matrix of size 5431 x 329.

References

David et al. (2014) Host lifestyle affects human microbiota on daily timescales Genome Biology vol. 15 (7):R89 Genome Biology

Examples

data(david_stoolA_otus)
  # sort OTUs by abundance
  sorted <- sort(apply(david_stoolA_otus,1,sum),
                 decreasing = TRUE, index.return = TRUE)
# display the top 10 most abundant OTUs
tsplot(david_stoolA_otus[sorted$ix[1:10],], header = "Stool A")

hallucigenia-sparsa/seqtime documentation built on Jan. 9, 2023, 11:53 p.m.